1
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Stare J. Oxidation of Flavin by Molecular Oxygen: Computational Insights into a Possible Radical Mechanism. ACS OMEGA 2024; 9:23431-23441. [PMID: 38854520 PMCID: PMC11154890 DOI: 10.1021/acsomega.4c00307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/19/2024] [Accepted: 05/13/2024] [Indexed: 06/11/2024]
Abstract
As a highly electrophilic moiety capable of oxidizing a variety of small organic molecules and biomolecules, flavin is an important prosthetic group in many enzymes. Upon oxidation of the substrate, flavin is converted into its reduced (dihydrogenated) form. The catalytic cycle is completed through oxidation back to the oxidized form, thus restoring the enzyme's oxidizing capability. While it has been firmly established that oxidation of the reduced form of flavin is cast by molecular oxygen, yielding oxidized flavin and hydrogen peroxide, the mechanism of this process is still poorly understood. Herein, we investigate the radical mechanism, which is one of the possible reaction mechanisms, by quantum chemical calculations. Because molecular oxygen exists as a triplet in its electronic ground state, whereas the products are singlets, the reaction is accompanied by hopping between electronic surfaces. We find that the rate-limiting factor of flavin oxidation is likely associated with the change in the spin state of the system. By considering several possible reactions involving flavin and its derivatives in the radical form and by examining the corresponding parts of the potential energy surface in various spin states, we estimate the effective barrier of the kinetically and thermodynamically preferred variant of flavin oxidation to be about 15 kcal/mol in the gas phase and about 7 kcal/mol in a polar (aqueous) environment. This is in agreement with kinetic studies of the corresponding monoamine oxidase enzymes, confirming the radical mechanism as a viable option for flavin regeneration in enzymes.
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Affiliation(s)
- Jernej Stare
- National Institute of Chemistry,Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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2
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Buda O, Hostiuc S, Popa-Velea O, Boroghina S. Altered states, alkaloids, and catatonia: Monoaminoxidase inhibitors and their role in the history of psychopharmacology. Front Pharmacol 2022; 13:1053534. [PMID: 36561338 PMCID: PMC9764005 DOI: 10.3389/fphar.2022.1053534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022] Open
Abstract
Monoamine oxidases are mitochondrial enzymes that catalyze the oxidative deamination of biogenic amines (adrenaline, noradrenaline, serotonin, and dopamine), causing their inactivation and subsequently playing a fundamental role in the homeostasis of various neurotransmitters. As the regulation of these effects was deemed important in clinical practice, numerous modulators of these enzymes were tested for various clinical effects. The purpose of this paper is to present a few historical landmarks regarding monoaminoxidase inhibitors and their usefulness as psychopharmacological agents. We will be focusing on banisterine, iproniazid, selegiline, rasagiline, tranylcypromine, moclobemide, and their role in the history of psychopharmacology. An almost unknown fact is that harmine, an MAO-A alkaloid, was used as early as the latter half of the 1920s in Bucharest, to reduce catatonic symptoms in schizophrenia, thus ushering the dawn of psychopharmacology era which started with chlorpromazine in the 1950s.
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Affiliation(s)
- Octavian Buda
- Department of History of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania,*Correspondence: Octavian Buda,
| | - Sorin Hostiuc
- Legal Medicine Department, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Ovidiu Popa-Velea
- Department of Medical Psychology, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Steluta Boroghina
- Department of History of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
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3
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In vitro and in silico investigation of inhibitory activities of 3-arylcoumarins and 3-phenylazo-4-hydroxycoumarin on MAO isoenzymes. Struct Chem 2022. [DOI: 10.1007/s11224-022-02092-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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4
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Meuwly M. Atomistic Simulations for Reactions and Vibrational Spectroscopy in the Era of Machine Learning─ Quo Vadis?. J Phys Chem B 2022; 126:2155-2167. [PMID: 35286087 DOI: 10.1021/acs.jpcb.2c00212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Atomistic simulations using accurate energy functions can provide molecular-level insight into functional motions of molecules in the gas and in the condensed phase. This Perspective delineates the present status of the field from the efforts of others and some of our own work and discusses open questions and future prospects. The combination of physics-based long-range representations using multipolar charge distributions and kernel representations for the bonded interactions is shown to provide realistic models for the exploration of the infrared spectroscopy of molecules in solution. For reactions, empirical models connecting dedicated energy functions for the reactant and product states allow statistically meaningful sampling of conformational space whereas machine-learned energy functions are superior in accuracy. The future combination of physics-based models with machine-learning techniques and integration into all-purpose molecular simulation software provides a unique opportunity to bring such dynamics simulations closer to reality.
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Affiliation(s)
- Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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5
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Why Monoamine Oxidase B Preferably Metabolizes N-Methylhistamine over Histamine: Evidence from the Multiscale Simulation of the Rate-Limiting Step. Int J Mol Sci 2022; 23:ijms23031910. [PMID: 35163835 PMCID: PMC8836602 DOI: 10.3390/ijms23031910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/04/2022] [Accepted: 02/05/2022] [Indexed: 11/18/2022] Open
Abstract
Histamine levels in the human brain are controlled by rather peculiar metabolic pathways. In the first step, histamine is enzymatically methylated at its imidazole Nτ atom, and the produced N-methylhistamine undergoes an oxidative deamination catalyzed by monoamine oxidase B (MAO-B), as is common with other monoaminergic neurotransmitters and neuromodulators of the central nervous system. The fact that histamine requires such a conversion prior to oxidative deamination is intriguing since MAO-B is known to be relatively promiscuous towards monoaminergic substrates; its in-vitro oxidation of N-methylhistamine is about 10 times faster than that for histamine, yet this rather subtle difference appears to be governing the decomposition pathway. This work clarifies the MAO-B selectivity toward histamine and N-methylhistamine by multiscale simulations of the rate-limiting hydride abstraction step for both compounds in the gas phase, in aqueous solution, and in the enzyme, using the established empirical valence bond methodology, assisted by gas-phase density functional theory (DFT) calculations. The computed barriers are in very good agreement with experimental kinetic data, especially for relative trends among systems, thereby reproducing the observed MAO-B selectivity. Simulations clearly demonstrate that solvation effects govern the reactivity, both in aqueous solution as well as in the enzyme although with an opposing effect on the free energy barrier. In the aqueous solution, the transition-state structure involving histamine is better solvated than its methylated analog, leading to a lower barrier for histamine oxidation. In the enzyme, the higher hydrophobicity of N-methylhistamine results in a decreased number of water molecules at the active side, leading to decreased dielectric shielding of the preorganized catalytic electrostatic environment provided by the enzyme. This renders the catalytic environment more efficient for N-methylhistamine, giving rise to a lower barrier relative to histamine. In addition, the transition state involving N-methylhistamine appears to be stabilized by the surrounding nonpolar residues to a larger extent than with unsubstituted histamine, contributing to a lower barrier with the former.
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6
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Qin Z, Yu S, Chen J, Zhou J. Dehydrogenases of acetic acid bacteria. Biotechnol Adv 2021; 54:107863. [PMID: 34793881 DOI: 10.1016/j.biotechadv.2021.107863] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 12/13/2022]
Abstract
Acetic acid bacteria (AAB) are a group of bacteria that can oxidize many substrates such as alcohols and sugar alcohols and play important roles in industrial biotechnology. A majority of industrial processes that involve AAB are related to their dehydrogenases, including PQQ/FAD-dependent membrane-bound dehydrogenases and NAD(P)+-dependent cytoplasmic dehydrogenases. These cofactor-dependent dehydrogenases must effectively regenerate their cofactors in order to function continuously. For PQQ, FAD and NAD(P)+ alike, regeneration is directly or indirectly related to the electron transport chain (ETC) of AAB, which plays an important role in energy generation for aerobic cell growth. Furthermore, in changeable natural habitats, ETC components of AAB can be regulated so that the bacteria survive in different environments. Herein, the progressive cascade in an application of AAB, including key dehydrogenases involved in the application, regeneration of dehydrogenase cofactors, ETC coupling with cofactor regeneration and ETC regulation, is systematically reviewed and discussed. As they have great application value, a deep understanding of the mechanisms through which AAB function will not only promote their utilization and development but also provide a reference for engineering of other industrial strains.
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Affiliation(s)
- Zhijie Qin
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shiqin Yu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jian Chen
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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7
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Zlobin A, Diankin I, Pushkarev S, Golovin A. Probing the Suitability of Different Ca 2+ Parameters for Long Simulations of Diisopropyl Fluorophosphatase. Molecules 2021; 26:5839. [PMID: 34641383 PMCID: PMC8510429 DOI: 10.3390/molecules26195839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022] Open
Abstract
Organophosphate hydrolases are promising as potential biotherapeutic agents to treat poisoning with pesticides or nerve gases. However, these enzymes often need to be further engineered in order to become useful in practice. One example of such enhancement is the alteration of enantioselectivity of diisopropyl fluorophosphatase (DFPase). Molecular modeling techniques offer a unique opportunity to address this task rationally by providing a physical description of the substrate-binding process. However, DFPase is a metalloenzyme, and correct modeling of metal cations is a challenging task generally coming with a tradeoff between simulation speed and accuracy. Here, we probe several molecular mechanical parameter combinations for their ability to empower long simulations needed to achieve a quantitative description of substrate binding. We demonstrate that a combination of the Amber19sb force field with the recently developed 12-6 Ca2+ models allows us to both correctly model DFPase and obtain new insights into the DFP binding process.
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Affiliation(s)
- Alexander Zlobin
- Faculty of Bioengineering, Lomonosov Moscow State University, 119234 Moscow, Russia; (I.D.); (S.P.)
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Igor Diankin
- Faculty of Bioengineering, Lomonosov Moscow State University, 119234 Moscow, Russia; (I.D.); (S.P.)
- Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Sergey Pushkarev
- Faculty of Bioengineering, Lomonosov Moscow State University, 119234 Moscow, Russia; (I.D.); (S.P.)
| | - Andrey Golovin
- Faculty of Bioengineering, Lomonosov Moscow State University, 119234 Moscow, Russia; (I.D.); (S.P.)
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Sirius University of Science and Technology, 354340 Sochi, Russia
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8
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Ostadkarampour M, Putnins EE. Monoamine Oxidase Inhibitors: A Review of Their Anti-Inflammatory Therapeutic Potential and Mechanisms of Action. Front Pharmacol 2021; 12:676239. [PMID: 33995107 PMCID: PMC8120032 DOI: 10.3389/fphar.2021.676239] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/06/2021] [Indexed: 12/18/2022] Open
Abstract
Chronic inflammatory diseases are debilitating, affect patients' quality of life, and are a significant financial burden on health care. Inflammation is regulated by pro-inflammatory cytokines and chemokines that are expressed by immune and non-immune cells, and their expression is highly controlled, both spatially and temporally. Their dysregulation is a hallmark of chronic inflammatory and autoimmune diseases. Significant evidence supports that monoamine oxidase (MAO) inhibitor drugs have anti-inflammatory effects. MAO inhibitors are principally prescribed for the management of a variety of central nervous system (CNS)-associated diseases such as depression, Alzheimer's, and Parkinson's; however, they also have anti-inflammatory effects in the CNS and a variety of non-CNS tissues. To bolster support for their development as anti-inflammatories, it is critical to elucidate their mechanism(s) of action. MAO inhibitors decrease the generation of end products such as hydrogen peroxide, aldehyde, and ammonium. They also inhibit biogenic amine degradation, and this increases cellular and pericellular catecholamines in a variety of immune and some non-immune cells. This decrease in end product metabolites and increase in catecholamines can play a significant role in the anti-inflammatory effects of MAO inhibitors. This review examines MAO inhibitor effects on inflammation in a variety of in vitro and in vivo CNS and non-CNS disease models, as well as their anti-inflammatory mechanism(s) of action.
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Affiliation(s)
- Mahyar Ostadkarampour
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, The University of British Columbia, Vancouver, BC, Canada
| | - Edward E Putnins
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, The University of British Columbia, Vancouver, BC, Canada
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9
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Muddapu VR, Chakravarthy VS. Influence of energy deficiency on the subcellular processes of Substantia Nigra Pars Compacta cell for understanding Parkinsonian neurodegeneration. Sci Rep 2021; 11:1754. [PMID: 33462293 PMCID: PMC7814067 DOI: 10.1038/s41598-021-81185-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 12/23/2020] [Indexed: 01/29/2023] Open
Abstract
Parkinson's disease (PD) is the second most prominent neurodegenerative disease around the world. Although it is known that PD is caused by the loss of dopaminergic cells in substantia nigra pars compacta (SNc), the decisive cause of this inexorable cell loss is not clearly elucidated. We hypothesize that "Energy deficiency at a sub-cellular/cellular/systems level can be a common underlying cause for SNc cell loss in PD." Here, we propose a comprehensive computational model of SNc cell, which helps us to understand the pathophysiology of neurodegeneration at the subcellular level in PD. The aim of the study is to see how deficits in the supply of energy substrates (glucose and oxygen) lead to a deficit in adenosine triphosphate (ATP). The study also aims to show that deficits in ATP are the common factor underlying the molecular-level pathological changes, including alpha-synuclein aggregation, reactive oxygen species formation, calcium elevation, and dopamine dysfunction. The model suggests that hypoglycemia plays a more crucial role in leading to ATP deficits than hypoxia. We believe that the proposed model provides an integrated modeling framework to understand the neurodegenerative processes underlying PD.
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Affiliation(s)
- Vignayanandam Ravindernath Muddapu
- grid.417969.40000 0001 2315 1926Computational Neuroscience Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Sardar Patel Road, Chennai, 600036 Tamil Nadu India
| | - V. Srinivasa Chakravarthy
- grid.417969.40000 0001 2315 1926Computational Neuroscience Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Sardar Patel Road, Chennai, 600036 Tamil Nadu India
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10
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Kubicskó K, Farkas Ö. Quantum chemical (QM:MM) investigation of the mechanism of enzymatic reaction of tryptamine and N,N-dimethyltryptamine with monoamine oxidase A. Org Biomol Chem 2020; 18:9660-9674. [PMID: 33215182 DOI: 10.1039/d0ob01118e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The endogenous psychedelic (mind-altering) N,N-dimethyltryptamine (DMT) molecule has an important role in tissue protection, regeneration, and immunity via sigma-1 receptor activation as its natural ligand. The immunologic properties of DMT suggest this biogenic compound should be investigated thoroughly in other aspects as well. In our in silico project, we examined the metabolism of DMT and its primary analogue, the tryptamine (T), by the monoamine oxidase (MAO) flavoenzyme. MAO has two isoforms, MAO-A and MAO-B. MAOs perform the oxidation of various monoamines by their flavin adenine dinucleotide (FAD) cofactor. Two-layer QM:MM calculations at the ONIOM(M06-2X/6-31++G(d,p):UFF=QEq) level were performed including the whole enzyme to explore the potential energy surface (PES) of the reactions. Our findings reinforced that a hybrid mechanism, a mixture of pure H+ and H- transfer pathways, describes precisely the rate-determining step of amine oxidation as suggested by earlier works. Additionally, our results show that the oxidation of tertiary amine DMT requires a lower activation barrier than the primary amine T. This may reflect a general rule, thus we recommend further investigations. Furthermore, we demonstrated that at pH 7.4 the protonated form of these substrates enter the enzyme. As the deprotonation of substrates is crucial, we presumed protonated cofactor, FADH+, may form. Surprisingly, the activation barriers are much lower compared to FAD with both substrates. Therefore, we suggest further investigations in this direction.
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Affiliation(s)
- Károly Kubicskó
- Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary.
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11
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Prah A, Purg M, Stare J, Vianello R, Mavri J. How Monoamine Oxidase A Decomposes Serotonin: An Empirical Valence Bond Simulation of the Reactive Step. J Phys Chem B 2020; 124:8259-8265. [PMID: 32845149 PMCID: PMC7520887 DOI: 10.1021/acs.jpcb.0c06502] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/26/2020] [Indexed: 12/15/2022]
Abstract
The enzyme-catalyzed degradation of the biogenic amine serotonin is an essential regulatory mechanism of its level in the human organism. In particular, monoamine oxidase A (MAO A) is an important flavoenzyme involved in the metabolism of monoamine neurotransmitters. Despite extensive research efforts, neither the catalytic nor the inhibition mechanisms of MAO enzymes are currently fully understood. In this article, we present the quantum mechanics/molecular mechanics simulation of the rate-limiting step for the serotonin decomposition, which consists of hydride transfer from the serotonin methylene group to the N5 atom of the flavin moiety. Free-energy profiles of the reaction were computed by the empirical valence bond method. Apart from the enzymatic environment, the reference reaction in the gas phase was also simulated, facilitating the estimation of the catalytic effect of the enzyme. The calculated barrier for the enzyme-catalyzed reaction of 14.82 ± 0.81 kcal mol-1 is in good agreement with the experimental value of 16.0 kcal mol-1, which provides strong evidence for the validity of the proposed hydride-transfer mechanism. Together with additional experimental and computational work, the results presented herein contribute to a deeper understanding of the catalytic mechanism of MAO A and flavoenzymes in general, and in the long run, they should pave the way toward applications in neuropsychiatry.
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Affiliation(s)
- Alja Prah
- Laboratory
for Computational Biochemistry and Drug Design, National Institute of Chemistry, Ljubljana 1001, Slovenia
- Faculty
of Pharmacy, University of Ljubljana, Ljubljana 1001, Slovenia
| | - Miha Purg
- Department
of Cell and Molecular Biology, Uppsala University, Uppsala SE-751 24, Sweden
| | - Jernej Stare
- Laboratory
for Computational Biochemistry and Drug Design, National Institute of Chemistry, Ljubljana 1001, Slovenia
| | - Robert Vianello
- Division
of Organic Chemistry and Biochemistry, Rud̵er
Bošković Institute, Zagreb 10002, Croatia
| | - Janez Mavri
- Laboratory
for Computational Biochemistry and Drug Design, National Institute of Chemistry, Ljubljana 1001, Slovenia
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12
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Hydride Abstraction as the Rate-Limiting Step of the Irreversible Inhibition of Monoamine Oxidase B by Rasagiline and Selegiline: A Computational Empirical Valence Bond Study. Int J Mol Sci 2020; 21:ijms21176151. [PMID: 32858935 PMCID: PMC7503497 DOI: 10.3390/ijms21176151] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/11/2020] [Accepted: 08/21/2020] [Indexed: 12/23/2022] Open
Abstract
Monoamine oxidases (MAOs) catalyze the degradation of a very broad range of biogenic and dietary amines including many neurotransmitters in the brain, whose imbalance is extensively linked with the biochemical pathology of various neurological disorders, and are, accordingly, used as primary pharmacological targets to treat these debilitating cognitive diseases. Still, despite this practical significance, the precise molecular mechanism underlying the irreversible MAO inhibition with clinically used propargylamine inhibitors rasagiline and selegiline is still not unambiguously determined, which hinders the rational design of improved inhibitors devoid of side effects current drugs are experiencing. To address this challenge, we present empirical valence bond QM/MM simulations of the rate-limiting step of the MAO inhibition involving the hydride anion transfer from the inhibitor α-carbon onto the N5 atom of the flavin adenin dinucleotide (FAD) cofactor. The proposed mechanism is strongly supported by the obtained free energy profiles, which confirm a higher reactivity of selegiline over rasagiline, while the calculated difference in the activation Gibbs energies of ΔΔG‡ = 3.1 kcal mol-1 is found to be in very good agreement with that from the measured literature kinact values that predict a 1.7 kcal mol-1 higher selegiline reactivity. Given the similarity with the hydride transfer mechanism during the MAO catalytic activity, these results verify that both rasagiline and selegiline are mechanism-based irreversible inhibitors and offer guidelines in designing new and improved inhibitors, which are all clinically employed in treating a variety of neuropsychiatric and neurodegenerative conditions.
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13
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Al-Obaidi A, Elmezayen AD, Yelekçi K. Homology modeling of human GABA-AT and devise some novel and potent inhibitors via computer-aided drug design techniques. J Biomol Struct Dyn 2020; 39:4100-4110. [PMID: 32462974 DOI: 10.1080/07391102.2020.1774417] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
γ-aminobutyric acid aminotransferase (GABA-AT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme which degrades γ-aminobutyric (GABA) in the brain. GABA is an important inhibitory neurotransmitter that plays important neurological roles in the brain. Therefore, GABA-AT is an important drug target which regulates the GABA level. Novel and potent drug development to inhibit GABA-AT is still very challenging task. In this study, we aimed to devise novel and potent inhibitors against GABA-AT using computer-aided drug design (CADD) tools. However, the human GABA-AT crystal structure is not available yet, and we built the 3D structure of human GABA-AT based on the crystal structure of pig's liver (Sus Scrofa) enzyme as a template. The generated model was validated with numerous tools such as ProSA and PROCHECK. A set of selected well-known inhibitors have been tested against the modeled GABA-AT. Molecular docking studies have been accomplished via application of Genetic Optimization for Ligand Docking (GOLD), Vina and Autodock 4.2 software to search for potent inhibitors. The best two candidate inhibitors have been computationally examined for absorption, distribution, metabolism, elimination and toxicity descriptors (ADMET) and Lipinski's rule of 5. Lastly, molecular dynamics (MD) simulations were carried out to inspect the ligands' binding mode and stability of the active site of human GABA-AT over time. The top ranked ligands exhibited reliable stability throughout the MD simulation. The selected compounds are promising candidates and might be tested experimentally for the inhibition of human GABA-AT enzyme. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anas Al-Obaidi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
| | - Ammar D Elmezayen
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
| | - Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
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14
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Prah A, Ogrin P, Mavri J, Stare J. Nuclear quantum effects in enzymatic reactions: simulation of the kinetic isotope effect of phenylethylamine oxidation catalyzed by monoamine oxidase A. Phys Chem Chem Phys 2020; 22:6838-6847. [DOI: 10.1039/d0cp00131g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By using computational techniques for quantizing nuclear motion one can accurately reproduce kinetic isotope effect of enzymatic reactions, as demonstrated for phenylethylamine oxidation catalyzed by the monoamine oxidase A enzyme.
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Affiliation(s)
- Alja Prah
- Theory Department
- National Institute of Chemistry
- Ljubljana
- Slovenia
- University of Ljubljana
| | - Peter Ogrin
- Theory Department
- National Institute of Chemistry
- Ljubljana
- Slovenia
- University of Ljubljana
| | - Janez Mavri
- Theory Department
- National Institute of Chemistry
- Ljubljana
- Slovenia
| | - Jernej Stare
- Theory Department
- National Institute of Chemistry
- Ljubljana
- Slovenia
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15
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Tandarić T, Vianello R. Computational Insight into the Mechanism of the Irreversible Inhibition of Monoamine Oxidase Enzymes by the Antiparkinsonian Propargylamine Inhibitors Rasagiline and Selegiline. ACS Chem Neurosci 2019; 10:3532-3542. [PMID: 31264403 DOI: 10.1021/acschemneuro.9b00147] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Monoamine oxidases (MAOs) are flavin adenine dinucleotide containing flavoenzymes that catalyze the degradation of a range of brain neurotransmitters, whose imbalance is extensively linked with the pathology of various neurological disorders. This is why MAOs have been the central pharmacological targets in treating neurodegeneration for more than 60 years. Still, despite this practical importance, the precise chemical mechanisms underlying the irreversible inhibition of the MAO B isoform with clinical drugs rasagiline (RAS) and selegiline (SEL) remained unknown. Here we employed a combination of MD simulations, MM-GBSA binding free energy evaluations, and QM cluster calculations to show the MAO inactivation proceeds in three steps, where, in the rate-limiting first step, FAD utilizes its N5 atom to abstracts a hydride anion from the inhibitor α-CH2 group to ultimately give the final inhibitor-FAD adduct matching crystallographic data. The obtained free energy profiles reveal a lower activation energy for SEL by 1.2 kcal mol-1 and a higher reaction exergonicity by 0.8 kcal mol-1, with the former being in excellent agreement with experimental ΔΔG‡EXP = 1.7 kcal mol-1, thus rationalizing its higher in vivo reactivity over RAS. The calculated ΔGBIND energies confirm SEL binds better due to its bigger size and flexibility allowing it to optimize hydrophobic C-H···π and π···π interactions with residues throughout both of enzyme's cavities, particularly with FAD, Gln206 and four active site tyrosines, thus overcoming a larger ability of RAS to form hydrogen bonds that only position it in less reactive orientations for the hydride abstraction. Offered results elucidate structural determinants affecting the affinity and rates of the inhibition reaction that should be considered to cooperate when designing more effective compounds devoid of untoward effects, which are of utmost significance and urgency with the growing prevalence of brain diseases.
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Affiliation(s)
- Tana Tandarić
- Computational Organic Chemistry and Biochemistry Group, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Robert Vianello
- Computational Organic Chemistry and Biochemistry Group, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
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16
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Calixto AR, Ramos MJ, Fernandes PA. Conformational diversity induces nanosecond-timescale chemical disorder in the HIV-1 protease reaction pathway. Chem Sci 2019; 10:7212-7221. [PMID: 31588289 PMCID: PMC6677113 DOI: 10.1039/c9sc01464k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/10/2019] [Indexed: 02/04/2023] Open
Abstract
The role of conformational diversity in enzyme catalysis has been a matter of analysis in recent studies. Pre-organization of the active site has been pointed out as the major source for enzymes' catalytic power. Following this line of thought, it is becoming clear that specific, instantaneous, non-rare enzyme conformations that make the active site perfectly pre-organized for the reaction lead to the lowest activation barriers that mostly contribute to the macroscopically observed reaction rate. The present work is focused on exploring the relationship between structure and catalysis in HIV-1 protease (PR) with an adiabatic mapping method, starting from different initial structures, collected from a classical MD simulation. The first, rate-limiting step of the HIV-1 PR catalytic mechanism was studied with the ONIOM QM/MM methodology (B3LYP/6-31G(d):ff99SB), with activation and reaction energies calculated at the M06-2X/6-311++G(2d,2p):ff99SB level of theory, in 19 different enzyme:substrate conformations. The results showed that the instantaneous enzyme conformations have two independent consequences on the enzyme's chemistry: they influence the barrier height, something also observed in the past in other enzymes, and they also influence the specific reaction pathway, which is something unusual and unexpected, challenging the "one enzyme-one substrate-one reaction mechanism" paradigm. Two different reaction mechanisms, with similar reactant probabilities and barrier heights, lead to the same gem-diol intermediate. Subtle nanosecond-timescale rearrangements in the active site hydrogen bonding network were shown to determine which reaction the enzyme follows. We named this phenomenon chemical disorder. The results make us realize the unexpected mechanistic consequences of conformational diversity in enzymatic reactivity.
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Affiliation(s)
- Ana Rita Calixto
- UCIBIO@REQUIMTE , Departamento de Química e Bioquímica , Faculdade de Ciências Universidade do Porto , Rua do Campo Alegre s/n , 4169-007 Porto , Portugal .
| | - Maria João Ramos
- UCIBIO@REQUIMTE , Departamento de Química e Bioquímica , Faculdade de Ciências Universidade do Porto , Rua do Campo Alegre s/n , 4169-007 Porto , Portugal .
| | - Pedro Alexandrino Fernandes
- UCIBIO@REQUIMTE , Departamento de Química e Bioquímica , Faculdade de Ciências Universidade do Porto , Rua do Campo Alegre s/n , 4169-007 Porto , Portugal .
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17
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Role of introduced surface cysteine of NADH oxidase from Lactobacillus rhamnosus. Int J Biol Macromol 2019; 132:150-156. [DOI: 10.1016/j.ijbiomac.2019.03.168] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/10/2019] [Accepted: 03/25/2019] [Indexed: 12/15/2022]
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18
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Umek N, Geršak B, Vintar N, Šoštarič M, Mavri J. Dopamine Autoxidation Is Controlled by Acidic pH. Front Mol Neurosci 2018; 11:467. [PMID: 30618616 PMCID: PMC6305604 DOI: 10.3389/fnmol.2018.00467] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/03/2018] [Indexed: 11/16/2022] Open
Abstract
We studied the reaction mechanism of dopamine autoxidation using quantum chemical methods. Unlike other biogenic amines important in the central nervous system, dopamine and noradrenaline are capable of undergoing a non-enzymatic autoxidative reaction giving rise to a superoxide anion that further decomposes to reactive oxygen species. The reaction in question, which takes place in an aqueous solution, is as such not limited to the mitochondrial membrane where scavenging enzymes such as catalase and superoxide dismutase are located. With the experimental rate constant of 0.147 s−1, the dopamine autoxidation reaction is comparably as fast as the monoamine oxidase B catalyzed dopamine decomposition with a rate constant of 1 s−1. By using quantum chemical calculations, we demonstrated that the rate-limiting step is the formation of a hydroxide ion from a water molecule, which attacks the amino group that enters intramolecular Michael addition, giving rise to a pharmacologically inert aminochrome. We have shown that for dopamine stability on a time scale of days, it is essential that the pH value of the synaptic vesicle interior is acidic. The pathophysiologic correlates of the results are discussed in the context of Parkinson's disease as well as the pathology caused by long-term amphetamine and cocaine administration.
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Affiliation(s)
- Nejc Umek
- Department of Anesthesiology and Surgical Intensive Therapy, University Medical Centre Ljubljana, Ljubljana, Slovenia.,Institute of Anatomy, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Blaž Geršak
- Department of Anesthesiology and Surgical Intensive Therapy, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Neli Vintar
- Department of Anesthesiology and Surgical Intensive Therapy, University Medical Centre Ljubljana, Ljubljana, Slovenia.,Department of Anesthesiology and Reanimatology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Šoštarič
- Department of Anesthesiology and Surgical Intensive Therapy, University Medical Centre Ljubljana, Ljubljana, Slovenia.,Department of Anesthesiology and Reanimatology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Janez Mavri
- National Institute of Chemistry, Ljubljana, Slovenia
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19
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Maršavelski A, Petrović D, Bauer P, Vianello R, Kamerlin SCL. Empirical Valence Bond Simulations Suggest a Direct Hydride Transfer Mechanism for Human Diamine Oxidase. ACS OMEGA 2018; 3:3665-3674. [PMID: 30023875 PMCID: PMC6044848 DOI: 10.1021/acsomega.8b00346] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/19/2018] [Indexed: 06/08/2023]
Abstract
Diamine oxidase (DAO) is an enzyme involved in the regulation of cell proliferation and the immune response. This enzyme performs oxidative deamination in the catabolism of biogenic amines, including, among others, histamine, putrescine, spermidine, and spermine. The mechanistic details underlying the reductive half-reaction of the DAO-catalyzed oxidative deamination which leads to the reduced enzyme cofactor and the aldehyde product are, however, still under debate. The catalytic mechanism was proposed to involve a prototropic shift from the substrate-Schiff base to the product-Schiff base, which includes the rate-limiting cleavage of the Cα-H bond by the conserved catalytic aspartate. Our detailed mechanistic study, performed using a combined quantum chemical cluster approach with empirical valence bond simulations, suggests that the rate-limiting cleavage of the Cα-H bond involves direct hydride transfer to the topaquinone cofactor-a mechanism that does not involve the formation of a Schiff base. Additional investigation of the D373E and D373N variants supported the hypothesis that the conserved catalytic aspartate is indeed essential for the reaction; however, it does not appear to serve as the catalytic base, as previously suggested. Rather, the electrostatic contributions of the most significant residues (including D373), together with the proximity of the Cu2+ cation to the reaction site, lower the activation barrier to drive the chemical reaction.
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Affiliation(s)
- Aleksandra Maršavelski
- Computational
Organic Chemistry and Biochemistry Group, Division of Organic Chemistry
and Biochemistry, Ruđer Bošković
Institute, Bijenička
cesta 54, 10000 Zagreb, Croatia
- Department
of Chemistry, Faculty of Science, University
of Zagreb, Horvatovac
102a, 10000 Zagreb, Croatia
- Department
of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Dušan Petrović
- Department
of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Paul Bauer
- Department
of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
- Department
of Biophysics, SciLifeLab, KTH Royal Institute
of Technology, S-10691 Stockholm, Sweden
| | - Robert Vianello
- Computational
Organic Chemistry and Biochemistry Group, Division of Organic Chemistry
and Biochemistry, Ruđer Bošković
Institute, Bijenička
cesta 54, 10000 Zagreb, Croatia
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20
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Pregeljc D, Jug U, Mavri J, Stare J. Why does the Y326I mutant of monoamine oxidase B decompose an endogenous amphetamine at a slower rate than the wild type enzyme? Reaction step elucidated by multiscale molecular simulations. Phys Chem Chem Phys 2018; 20:4181-4188. [PMID: 29360121 DOI: 10.1039/c7cp07069a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This work investigates the Y326I point mutation effect on the kinetics of oxidative deamination of phenylethylamine (PEA) catalyzed by the monoamine oxidase B (MAO B) enzyme. PEA is a neuromodulator capable of affecting the plasticity of the brain and is responsible for the mood enhancing effect caused by physical exercise. Due to a similar functionality, PEA is often regarded as an endogenous amphetamine. The rate limiting step of the deamination was simulated at the multiscale level, employing the Empirical Valence Bond approach for the quantum treatment of the involved valence states, whereas the environment (solvated protein) was represented with a classical force field. A comparison of the reaction free energy profiles delivered by simulation of the reaction in the wild type MAO B and its Y326I mutant yields an increase in the barrier by 1.06 kcal mol-1 upon mutation, corresponding to a roughly 6-fold decrease in the reaction rate. This is in excellent agreement with the experimental kinetic studies. Inspection of simulation trajectories reveals possible sources of the point mutation effect, namely vanishing favorable electrostatic interactions between PEA and a Tyr326 side chain and an increased amount of water molecules at the active site due to the replacement of tyrosine by a less spacious isoleucine residue, thereby increasing the dielectric shielding of the catalytic environment provided by the enzyme.
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Affiliation(s)
- Domen Pregeljc
- Theory Department, National Institute of Chemistry, Ljubljana, Slovenia.
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21
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Yang Z, Chen J, Zhou Y, Huang H, Xu D, Zhang C. Understanding the hydrogen transfer mechanism for the biodegradation of 2,4,6-trinitrotoluene catalyzed by pentaerythritol tetranitrate reductase: molecular dynamics simulations. Phys Chem Chem Phys 2018; 20:12157-12165. [DOI: 10.1039/c8cp00345a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The explosive 2,4,6-trinitrotoluene (TNT) is a highly toxic pollutant.
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Affiliation(s)
- Zhilin Yang
- Institute of Chemical Materials
- Chinese Academy of Engineering and Physics
- 621900 Mianyang
- China
| | - Junxian Chen
- MOE Key Laboratory of Green Chemistry & Technology
- College of Chemistry
- Sichuan University
- Chengdu
- P. R. China
| | - Yang Zhou
- Institute of Chemical Materials
- Chinese Academy of Engineering and Physics
- 621900 Mianyang
- China
| | - Hui Huang
- Institute of Chemical Materials
- Chinese Academy of Engineering and Physics
- 621900 Mianyang
- China
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry & Technology
- College of Chemistry
- Sichuan University
- Chengdu
- P. R. China
| | - Chaoyang Zhang
- Institute of Chemical Materials
- Chinese Academy of Engineering and Physics
- 621900 Mianyang
- China
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22
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The design of target specific antibodies (scFv) by applying de novo workflow: Case study on BmR1 antigen from Brugia malayi. J Mol Graph Model 2017; 76:543-550. [DOI: 10.1016/j.jmgm.2017.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 06/02/2017] [Accepted: 07/05/2017] [Indexed: 11/24/2022]
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23
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Elementary S N 2 reaction revisited. Effects of solvent and alkyl chain length on kinetics of halogen exchange in haloalkanes elucidated by Empirical Valence Bond simulation. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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24
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Oanca G, Stare J, Mavri J. How fast monoamine oxidases decompose adrenaline? Kinetics of isoenzymes A and B evaluated by empirical valence bond simulation. Proteins 2017; 85:2170-2178. [PMID: 28836294 DOI: 10.1002/prot.25374] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/18/2017] [Accepted: 08/21/2017] [Indexed: 12/22/2022]
Abstract
This work scrutinizes kinetics of decomposition of adrenaline catalyzed by monoamine oxidase (MAO) A and B enzymes, a process controlling the levels of adrenaline in the central nervous system and other tissues. Experimental kinetic data for MAO A and B catalyzed decomposition of adrenaline are reported only in the form of the maximum reaction rate. Therefore, we estimated the experimental free energy barriers form the kinetic data of closely related systems using regression method, as was done in our previous study. By using multiscale simulation on the Empirical Valence Bond (EVB) level, we studied the chemical reactivity of the MAO A catalyzed decomposition of adrenaline and we obtained a value of activation free energy of 17.3 ± 0.4 kcal/mol. The corresponding value for MAO B is 15.7 ± 0.7 kcal/mol. Both values are in good agreement with the estimated experimental barriers of 16.6 and 16.0 kcal/mol for MAO A and MAO B, respectively. The fact that we reproduced the kinetic data and preferential catalytic effect of MAO B over MAO A gives additional support to the validity of the proposed hydride transfer mechanism. Furthermore, we demonstrate that adrenaline is preferably involved in the reaction in a neutral rather than in a protonated form due to considerably higher barriers computed for the protonated adrenaline substrate. The results are discussed in the context of chemical mechanism of MAO enzymes and possible applications of multiscale simulation to rationalize the effects of MAO activity on adrenaline level.
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Affiliation(s)
- Gabriel Oanca
- Department of Computational Biochemistry and Drug Design, National Institute of Chemistry, Ljubljana, Slovenia.,Faculty of Physics, Alexandru Ioan Cuza University of Iasi, Iasi, Romania
| | - Jernej Stare
- Department of Computational Biochemistry and Drug Design, National Institute of Chemistry, Ljubljana, Slovenia
| | - Janez Mavri
- Department of Computational Biochemistry and Drug Design, National Institute of Chemistry, Ljubljana, Slovenia
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25
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Multiscale simulation of monoamine oxidase catalyzed decomposition of phenylethylamine analogs. Eur J Pharmacol 2017; 817:46-50. [PMID: 28583428 DOI: 10.1016/j.ejphar.2017.05.061] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 03/31/2017] [Accepted: 05/31/2017] [Indexed: 01/01/2023]
Abstract
Phenylethylamine (PEA) is an endogenous amphetamine and its levels are increased by physical activity. As other biogenic monoamines, it is decomposed by monoamine oxidase (MAO) enzymes. The chemical mechanism of MAO, and flavoenzymes in general, is a subject of heated debate. We have previously shown that the rate-limiting step of MAO catalysis involves a hydride transfer from the substrate methylene group vicinal to the amino group to the N5 atom of the lumiflavin co-factor moiety. By using multiscale simulation on the Empirical Valence Bond (EVB) level, we studied the chemical reactivity of the monoamine oxidase B catalyzed decomposition of PEA and its two derivatives: p-chloro-β-methylphenylamine (p-CMP) and p-methoxy-β-methylphenethylamine (p-MMP). We calculated activation free energies of 17.1kcal/mol (PEA), 18.4kcal/mol (p-MMP) and 20.0kcal/mol (p-CMP), which are in excellent agreement with the experimental values of 16.7kcal/mol for PEA and 18.3kcal/mol for p-MMP, while the experimental value for p-CMP is not available. This gives strong support to the validity of our hydride transfer mechanism for both MAO A and B isoforms. The results are discussed in the context of the interplay between MAO point mutations and neuropsychiatric disorders.
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26
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Khan MKA, Akhtar S, Arif JM. Development of In Silico Protocols to Predict Structural Insights into the Metabolic Activation Pathways of Xenobiotics. Interdiscip Sci 2017; 10:329-345. [PMID: 28527150 DOI: 10.1007/s12539-017-0237-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 05/05/2017] [Accepted: 05/09/2017] [Indexed: 11/26/2022]
Abstract
To establish in silico model to predict the structural insight into the metabolic bioactivation pathway of xenobiotics, we considered two specific and one non-specific mammary procarcinogen [e.g., dibenzo[a,l]pyrene (DBP), 7,12-dimethylbenz[a]anthracene (DMBA), and benzo[a]pyrene (BP)]. The CYP1A1, 1B1, 2C9, 1A2 and 2B6 reported in wet-lab studies to actively metabolize DBP also showed strong binding energies (kcal/mol) of -11.50, -10.67, -10.37, -9.76 and -9.72, respectively, with inhibition constants ranging between 0.01 and 0.08 µM. The CYP3A4 depicted minimum binding energy (-9.51 kcal/mol) which is in agreement with the wet-lab reports. Further, relatively better affinity of CYP1A1 and CYP1B1 with the dibenzo[a,l]pyrene-11,12-diol (DBPD) might be indicative of their involvement in carcinogenicity of parent compound. Like DBP, BP (-10.13 kcal/mol, Ki: 0.04 µM) and BP-diols (BPD) (-9.01 kcal/mol, Ki: 0.25 µM) observed plausible binding with CYP1A1 supporting to the reported data that emphasize the major contribution of CYP1A1 in the activation of similar procarcinogens and mutagens. Likewise, in silico results further highlighted the CYP1A1 as key player in bioactivation of DMBA to its carcinogenic metabolites. In case of PhIP metabolism, strong binding interaction predicted with CYP1A1 (-9.63 kcal/mol) rather than CYP1A2 (-8.84 kcal/mol). Dissimilarity in the binding affinity of PhIP might be due to its basic scaffold. Further, molecular dynamics (MD) simulation of 10 ns has been revealed that docked complexes of CYP1A1 with DBP, DMBA and BP are comparatively more stable than the complex of PhIP. Moreover, the current findings might be valuable as reference model in prediction and elucidation of the approximate metabolic pathway of xenobiotics.
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Affiliation(s)
- M Kalim A Khan
- Department of Bioengineering, Faculty of Engineering, Integral University, Lucknow, 226026, India
| | - Salman Akhtar
- Department of Bioengineering, Faculty of Engineering, Integral University, Lucknow, 226026, India
| | - Jamal M Arif
- Department of Biosciences, Faculty of Applied Sciences, Integral University, Kursi Road, P.O. Box Basha, Lucknow, 226026, India.
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27
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Maršavelski A, Vianello R. What a Difference a Methyl Group Makes: The Selectivity of Monoamine Oxidase B Towards Histamine and N-Methylhistamine. Chemistry 2017; 23:2915-2925. [PMID: 28052533 DOI: 10.1002/chem.201605430] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Indexed: 12/17/2022]
Abstract
Monoamine oxidase (MAO) enzymes catalyze the degradation of a very broad range of biogenic and dietary amines including many neurotransmitters in the brain, whose imbalance is extensively linked with the biochemical pathology of various neurological disorders. Although sharing around 70 % sequence identity, both MAO A and B isoforms differ in substrate affinities and inhibitor sensitivities. Inhibitors that act on MAO A are used to treat depression, due to their ability to raise serotonin concentrations, whereas MAO B inhibitors decrease dopamine degradation and improve motor control in patients with Parkinson disease. Despite this functional importance, the factors affecting MAO selectivity are poorly understood. Here, we used a combination of molecular dynamics (MD) simulations, molecular mechanics with Poisson-Boltzmann and surface area solvation (MM-PBSA) binding free energy evaluations, and quantum mechanical (QM) cluster calculations to address the unexpected, yet challenging MAO B selectivity for N-methylhistamine (NMH) over histamine (HIS), differing only in a single methyl group distant from the reactive ethylamino center. This study shows that a dominant selectivity contribution is offered by a lower activation free energy for NMH by 2.6 kcal mol-1 , in excellent agreement with the experimental ΔΔG≠EXP =1.4 kcal mol-1 , together with a more favorable reaction exergonicity and active-site binding. This study also confirms the hydrophobic nature of the MAO B active site and underlines the important role of Ile199, Leu171, and Leu328 in properly orienting substrates for the reaction.
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Affiliation(s)
- Aleksandra Maršavelski
- Computational Organic Chemistry and Biochemistry Group, Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia
| | - Robert Vianello
- Computational Organic Chemistry and Biochemistry Group, Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia
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28
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Sjögren T, Wassvik CM, Snijder A, Aagaard A, Kumanomidou T, Barlind L, Kaminski TP, Kashima A, Yokota T, Fjellström O. The Structure of Murine N 1-Acetylspermine Oxidase Reveals Molecular Details of Vertebrate Polyamine Catabolism. Biochemistry 2017; 56:458-467. [PMID: 28029774 DOI: 10.1021/acs.biochem.6b01140] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
N1-Acetylspermine oxidase (APAO) catalyzes the conversion of N1-acetylspermine or N1-acetylspermidine to spermidine or putrescine, respectively, with concomitant formation of N-acetyl-3-aminopropanal and hydrogen peroxide. Here we present the structure of murine APAO in its oxidized holo form and in complex with substrate. The structures provide a basis for understanding molecular details of substrate interaction in vertebrate APAO, highlighting a key role for an asparagine residue in coordinating the N1-acetyl group of the substrate. We applied computational methods to the crystal structures to rationalize previous observations with regard to the substrate charge state. The analysis suggests that APAO features an active site ideally suited for binding of charged polyamines. We also reveal the structure of APAO in complex with the irreversible inhibitor MDL72527. In addition to the covalent adduct, a second MDL72527 molecule is bound in the active site. Binding of MDL72527 is accompanied by altered conformations in the APAO backbone. On the basis of structures of APAO, we discuss the potential for development of specific inhibitors.
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Affiliation(s)
- Tove Sjögren
- Discovery Sciences, Innovative Medicines and Early Development, AstraZeneca , Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | - Carola M Wassvik
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development, AstraZeneca , Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | - Arjan Snijder
- Discovery Sciences, Innovative Medicines and Early Development, AstraZeneca , Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | - Anna Aagaard
- Discovery Sciences, Innovative Medicines and Early Development, AstraZeneca , Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | - Taichi Kumanomidou
- Discovery Technology Laboratories, Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation , 1000, Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | - Louise Barlind
- Discovery Sciences, Innovative Medicines and Early Development, AstraZeneca , Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | - Tim P Kaminski
- Discovery Sciences, Innovative Medicines and Early Development, AstraZeneca , Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | - Akiko Kashima
- Discovery Technology Laboratories, Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation , 1000, Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | - Takehiro Yokota
- Discovery Technology Laboratories, Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation , 1000, Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | - Ola Fjellström
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development, AstraZeneca , Pepparedsleden 1, SE-431 83 Mölndal, Sweden
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29
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Stare J. Complete sampling of an enzyme reaction pathway: a lesson from gas phase simulations. RSC Adv 2017. [DOI: 10.1039/c6ra27894a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
With proper sampling strategy, convergence of free energy profiles of biomolecular reactions in the gas phase can be achieved in microseconds of simulation.
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Affiliation(s)
- Jernej Stare
- Department of Computational Biochemistry and Drug Design
- National Institute of Chemistry
- SI-1000 Ljubljana
- Slovenia
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30
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Poberžnik M, Purg M, Repič M, Mavri J, Vianello R. Empirical Valence Bond Simulations of the Hydride-Transfer Step in the Monoamine Oxidase A Catalyzed Metabolism of Noradrenaline. J Phys Chem B 2016; 120:11419-11427. [PMID: 27734680 DOI: 10.1021/acs.jpcb.6b09011] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Monoamine oxidases (MAOs) A and B are flavoenzymes responsible for the metabolism of biogenic amines, such as dopamine, serotonin, and noradrenaline (NA), which is why they have been extensively implicated in the etiology and course of various neurodegenerative disorders and, accordingly, used as primary pharmacological targets to treat these debilitating cognitive diseases. The precise chemical mechanism through which MAOs regulate the amine concentration, which is vital for the development of novel inhibitors, is still not unambiguously determined in the literature. In this work, we present atomistic empirical valence bond simulations of the rate-limiting step of the MAO-A-catalyzed NA (norepinephrine) degradation, involving hydride transfer from the substrate α-methylene group to the flavin moiety of the flavin adenine dinucleotide prosthetic group, employing the full dimensionality and thermal fluctuations of the hydrated enzyme, with extensive configurational sampling. We show that MAO-A lowers the free energy of activation by 14.3 kcal mol-1 relative to that of the same reaction in aqueous solution, whereas the calculated activation free energy of ΔG‡ = 20.3 ± 1.6 kcal mol-1 is found to be in reasonable agreement with the correlated experimental value of 16.5 kcal mol-1. The results presented here strongly support the fact that both MAO-A and MAO-B isoforms function by the same hydride-transfer mechanism. We also considered a few point mutations of the "aromatic cage" tyrosine residue (Tyr444Phe, Tyr444Leu, Tyr444Trp, Tyr444His, and Tyr444Glu), and the calculated changes in the reaction barriers are in agreement with the experimental values, thus providing further support to the proposed mechanism.
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Affiliation(s)
- Matic Poberžnik
- Department of Physical and Organic Chemistry, Jožef Stefan Institute , Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Miha Purg
- Department of Cell and Molecular Biology, Uppsala Biomedical Centre , Husargatan 3, S-75124 Uppsala, Sweden
| | - Matej Repič
- Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry , Hajdrihova ulica 19, SI-1000 Ljubljana, Slovenia
| | - Janez Mavri
- Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry , Hajdrihova ulica 19, SI-1000 Ljubljana, Slovenia
| | - Robert Vianello
- Computational Organic Chemistry and Biochemistry Group, Ruđer Bošković Institute , Bijenička cesta 54, HR-10000 Zagreb, Croatia
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31
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Abstract
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Although QM/MM calculations
are the primary current tool for modeling enzymatic reactions, the
reliability of such calculations can be limited by the size of the
QM region. Thus, we examine in this work the dependence of QM/MM calculations
on the size of the QM region, using the reaction of catechol-O-methyl transferase (COMT) as a test case. Our study focuses
on the effect of adding residues to the QM region on the activation
free energy, obtained with extensive QM/MM sampling. It is found that
the sensitivity of the activation barrier to the size of the QM is
rather limited, while the dependence of the reaction free energy is
somewhat larger. Of course, the results depend on the inclusion of
the first solvation shell in the QM regions. For example, the inclusion
of the Mg2+ ion can change the activation barrier due to
charge transfer effects. However, such effects can easily be included
in semiempirical approaches by proper parametrization. Overall, we
establish that QM/MM calculations of activation barriers of enzymatic
reactions are not highly sensitive to the size of the QM region, beyond
the immediate region that describes the reacting atoms.
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32
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Cakir K, Erdem SS, Atalay VE. ONIOM calculations on serotonin degradation by monoamine oxidase B: insight into the oxidation mechanism and covalent reversible inhibition. Org Biomol Chem 2016; 14:9239-9252. [PMID: 27605388 DOI: 10.1039/c6ob01175f] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Monoamine oxidase (MAO) is an enzyme which catalyzes the oxidation of neurotransmitter amines and regulates their level. There are two forms of the enzyme with 70% similarity, known as MAO-A and MAO-B. MAO inhibitors are used in the treatment of neurological disorders such as depression, Parkinson's and Alzheimer's diseases. Therefore, understanding the chemical steps of MAO catalyzed amine oxidation is crucial for rational drug design. However, despite many experimental studies and recent computational efforts in the literature, the amine oxidation mechanism by MAO enzymes is still controversial. The polar nucleophilic mechanism and hydride transfer mechanisms are under debate in recent QM/MM studies. In this study, the serotonin oxidation mechanism by MAO was explored via the ONIOM (QM : QM) methodology at the M06-2X/6-31+G(d,p):PM6 level. A modified MAO mechanism involving a covalent reversible inhibition step via formation of flavin N5 ylide was proposed. This mechanism can be used to modulate the potency and reversibility of novel mechanism-based covalent inhibitors by intelligent modifications of the structure of the inhibitors. NBO donor-acceptor analysis confirms that the rate-determining αC-H cleavage step is a hybrid of hydride and proton transfer where hydride transfer dominates over the proton transfer. The functional role of covalent FAD was also investigated by calculating the activation energy of noncovalent FAD models where a 22 fold decrease in the rate of catalysis was predicted. Geometrical features imply that the function of the covalent bond in FAD might be to maintain the correct geometry and conformation for a more efficient catalysis.
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Affiliation(s)
- Kubra Cakir
- Marmara University, Department of Chemistry, Faculty of Arts and Sciences, 34722 Göztepe, Istanbul, Turkey.
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33
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Billod JM, Saenz-Mendez P, Blomberg A, Eriksson LA. Structures, Properties, and Dynamics of Intermediates in eEF2-Diphthamide Biosynthesis. J Chem Inf Model 2016; 56:1776-86. [PMID: 27525663 DOI: 10.1021/acs.jcim.6b00223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The eukaryotic translation Elongation Factor 2 (eEF2) is an essential enzyme in protein synthesis. eEF2 contains a unique modification of a histidine (His699 in yeast; HIS) into diphthamide (DTA), obtained via 3-amino-3-carboxypropyl (ACP) and diphthine (DTI) intermediates in the biosynthetic pathway. This essential and unique modification is also vulnerable, in that it can be efficiently targeted by NAD(+)-dependent ADP-ribosylase toxins, such as diphtheria toxin (DT). However, none of the intermediates in the biosynthesis path is equally vulnerable against the toxins. This study aims to address the different susceptibility of DTA and its precursors against bacterial toxins. We have herein undertaken a detailed in silico study of the structural features and dynamic motion of different His699 intermediates along the diphthamide synthesis pathway (HIS, ACP, DTI, DTA). The study points out that DTA forms a strong hydrogen bond with an asparagine which might explain the ADP-ribosylation mechanism caused by the diphtheria toxin (DT). Finally, in silico mutagenesis studies were performed on the DTA modified protein, in order to hamper the formation of such a hydrogen bond. The results indicate that the mutant structure might in fact be less susceptible to attack by DT and thereby behave similarly to DTI in this respect.
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Affiliation(s)
- Jean-Marc Billod
- Department of Chemical and Physical Biology, Center for Biological Research, CIB-CSIC , 28040 Madrid, Spain
| | - Patricia Saenz-Mendez
- Computational Chemistry and Biology Group, Facultad de Química, Universidad de la República , 11800 Montevideo, Uruguay
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34
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Li LL, Li K, Liu YH, Xu HR, Yu XQ. Red emission fluorescent probes for visualization of monoamine oxidase in living cells. Sci Rep 2016; 6:31217. [PMID: 27499031 PMCID: PMC4976310 DOI: 10.1038/srep31217] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 07/14/2016] [Indexed: 12/20/2022] Open
Abstract
Here we report two novel red emission fluorescent probes for the highly sensitive and selective detection of monoamine oxidase (MAO) with large Stokes shift (227 nm). Both of the probes possess solid state fluorescence and can accomplish the identification of MAO on test papers. The probe MAO-Red-1 exhibited a detection limit down to 1.2 μg mL−1 towards MAO-B. Moreover, the cleavage product was unequivocally conformedby HPLC and LCMS and the result was in accordance with the proposed oxidative deamination mechanism. The excellent photostability of MAO-Red-1 was proved both in vitro and in vivo through fluorescent kinetic experiment and laser exposure experiment of confocal microscopy, respectively. Intracellular experiments also confirmed the low cytotoxity and exceptional cell imaging abilities of MAO-Red-1. It was validated both in HeLa and HepG2 cells that MAO-Red-1 was capable of reporting MAO activity through the variation of fluorescence intensity.
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Affiliation(s)
- Ling-Ling Li
- Key Laboratory of Green Chemistry and Technology, Ministry of Education,College of Chemistry, Sichuan University, No. 29, Wangjiang Road, Chengdu, 610064, P. R. China
| | - Kun Li
- Key Laboratory of Green Chemistry and Technology, Ministry of Education,College of Chemistry, Sichuan University, No. 29, Wangjiang Road, Chengdu, 610064, P. R. China
| | - Yan-Hong Liu
- Key Laboratory of Green Chemistry and Technology, Ministry of Education,College of Chemistry, Sichuan University, No. 29, Wangjiang Road, Chengdu, 610064, P. R. China
| | - Hao-Ran Xu
- Key Laboratory of Green Chemistry and Technology, Ministry of Education,College of Chemistry, Sichuan University, No. 29, Wangjiang Road, Chengdu, 610064, P. R. China
| | - Xiao-Qi Yu
- Key Laboratory of Green Chemistry and Technology, Ministry of Education,College of Chemistry, Sichuan University, No. 29, Wangjiang Road, Chengdu, 610064, P. R. China
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35
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Ramsay RR. Molecular aspects of monoamine oxidase B. Prog Neuropsychopharmacol Biol Psychiatry 2016; 69:81-9. [PMID: 26891670 DOI: 10.1016/j.pnpbp.2016.02.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 02/06/2016] [Accepted: 02/11/2016] [Indexed: 02/07/2023]
Abstract
Monoamine oxidases (MAO) influence the monoamine levels in brain by virtue of their role in neurotransmitter breakdown. MAO B is the predominant form in glial cells and in platelets. MAO B structure, function and kinetics are described as a background for the effect of alterations in its activity on behavior. The need to inhibit MAO B to combat decreased brain amines continues to drive the search for new drugs. Reversible and irreversible inhibitors are now designed using data-mining, computational screening, docking and molecular dynamics. Multi-target ligands designed to combat the elevated activity of MAO B in Alzheimer's and Parkinson's Diseases incorporate MAO inhibition (usually irreversible) as well as iron chelation, antioxidant or neuroprotective properties. The main focus of drug design is the catalytic activity of MAO, but the imidazoline I2 site in the entrance cavity of MAO B is also a pharmacological target. Endogenous regulation of MAO B expression is discussed briefly in light of new studies measuring mRNA, protein, or activity in healthy and degenerative samples, including the effect of DNA methylation on the expression. Overall, this review focuses on examples of recent research on the molecular aspects of the expression, activity, and inhibition of MAO B.
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Affiliation(s)
- Rona R Ramsay
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, United Kingdom.
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36
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Vianello R, Domene C, Mavri J. The Use of Multiscale Molecular Simulations in Understanding a Relationship between the Structure and Function of Biological Systems of the Brain: The Application to Monoamine Oxidase Enzymes. Front Neurosci 2016; 10:327. [PMID: 27471444 PMCID: PMC4945635 DOI: 10.3389/fnins.2016.00327] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 06/28/2016] [Indexed: 01/17/2023] Open
Abstract
HIGHLIGHTS Computational techniques provide accurate descriptions of the structure and dynamics of biological systems, contributing to their understanding at an atomic level.Classical MD simulations are a precious computational tool for the processes where no chemical reactions take place.QM calculations provide valuable information about the enzyme activity, being able to distinguish among several mechanistic pathways, provided a carefully selected cluster model of the enzyme is considered.Multiscale QM/MM simulation is the method of choice for the computational treatment of enzyme reactions offering quantitative agreement with experimentally determined reaction parameters.Molecular simulation provide insight into the mechanism of both the catalytic activity and inhibition of monoamine oxidases, thus aiding in the rational design of their inhibitors that are all employed and antidepressants and antiparkinsonian drugs. Aging society and therewith associated neurodegenerative and neuropsychiatric diseases, including depression, Alzheimer's disease, obsessive disorders, and Parkinson's disease, urgently require novel drug candidates. Targets include monoamine oxidases A and B (MAOs), acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and various receptors and transporters. For rational drug design it is particularly important to combine experimental synthetic, kinetic, toxicological, and pharmacological information with structural and computational work. This paper describes the application of various modern computational biochemistry methods in order to improve the understanding of a relationship between the structure and function of large biological systems including ion channels, transporters, receptors, and metabolic enzymes. The methods covered stem from classical molecular dynamics simulations to understand the physical basis and the time evolution of the structures, to combined QM, and QM/MM approaches to probe the chemical mechanisms of enzymatic activities and their inhibition. As an illustrative example, the later will focus on the monoamine oxidase family of enzymes, which catalyze the degradation of amine neurotransmitters in various parts of the brain, the imbalance of which is associated with the development and progression of a range of neurodegenerative disorders. Inhibitors that act mainly on MAO A are used in the treatment of depression, due to their ability to raise serotonin concentrations, while MAO B inhibitors decrease dopamine degradation and improve motor control in patients with Parkinson disease. Our results give strong support that both MAO isoforms, A and B, operate through the hydride transfer mechanism. Relevance of MAO catalyzed reactions and MAO inhibition in the context of neurodegeneration will be discussed.
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Affiliation(s)
- Robert Vianello
- Computational Organic Chemistry and Biochemistry Group, Ruđer Bošković InstituteZagreb, Croatia
| | - Carmen Domene
- Department of Chemistry, King's College LondonLondon, UK
- Chemistry Research Laboratory, University of OxfordOxford, UK
| | - Janez Mavri
- Department of Computational Biochemistry and Drug Design, National Institute of ChemistryLjubljana, Slovenia
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37
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Fierro A, Edmondson DE, Celis-Barros C, Rebolledo-Fuentes M, Zapata-Torres G. Why p-OMe- and p-Cl-β-Methylphenethylamines Display Distinct Activities upon MAO-B Binding. PLoS One 2016; 11:e0154989. [PMID: 27152414 PMCID: PMC4859490 DOI: 10.1371/journal.pone.0154989] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 04/23/2016] [Indexed: 12/16/2022] Open
Abstract
Despite their structural and chemical commonalities, p-chloro-β-methylphenethylamine and p-methoxy-β-methylphenethylamine display distinct inhibitory and substrate activities upon MAO-B binding. Density Functional Theory (DFT) quantum chemical calculations reveal that β-methylation and para-substitution underpin the observed activities sustained by calculated transition state energy barriers, attained conformations and key differences in their interactions in the enzyme’s substrate binding site. Although both compounds meet substrate requirements, it is clear that β-methylation along with the physicochemical features of the para-substituents on the aromatic ring determine the activity of these compounds upon binding to the MAO B-isoform. While data for a larger set of compounds might lend generality to our conclusions, our experimental and theoretical results strongly suggest that the contrasting activities displayed depend on the conformations adopted by these compounds when they bind to the enzyme.
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Affiliation(s)
- Angélica Fierro
- Facultad de Química, Departamento de Química Orgánica, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Dale E. Edmondson
- Departments of Chemistry and Biochemistry, Emory University, Atlanta, GA, United States of America
| | - Cristian Celis-Barros
- Universidad Andres Bello, Facultad de Ciencias Exactas, Departamento de Ciencias Quimicas, Santiago, Chile
- * E-mail:
| | | | - Gerald Zapata-Torres
- Faculty of Chemical and Pharmaceutical Sciences, University of Chile, Santiago, Chile
- * E-mail:
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38
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Oanca G, Purg M, Mavri J, Shih JC, Stare J. Insights into enzyme point mutation effect by molecular simulation: phenylethylamine oxidation catalyzed by monoamine oxidase A. Phys Chem Chem Phys 2016; 18:13346-56. [PMID: 27121693 DOI: 10.1039/c6cp00098c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The I335Y point mutation effect on the kinetics of phenylethylamine decomposition catalyzed by monoamine oxidase A was elucidated by means of molecular simulation. The established empirical valence bond methodology was used in conjunction with the free energy perturbation sampling technique and a classical force field representing the state of reactants and products. The methodology allows for the simulation of chemical reactions, in the present case the breaking of the α-C-H bond in a phenylethylamine substrate and the subsequent hydrogen transfer to the flavin cofactor, resulting in the formation of the N-H bond on flavin. The empirical parameters were calibrated against the experimental data for the simulated reaction in a wild type protein and then used for the calculation of the reaction free energy profile in the I335Y mutant. In very good agreement with the measured kinetic data, mutation increases the free energy barrier for the rate limiting step by slightly more than 1 kcal mol(-1) and consequently decreases the rate constant by about an order of magnitude. The magnitude of the computed effect slightly varies with simulation settings, but always remains in reasonable agreement with the experiment. Analysis of trajectories reveals a major change in the interaction between phenyl rings of the substrate and the neighboring Phe352 residue upon the I335Y mutation due to the increased local polarity, leading to an attenuated quadrupole interaction between the rings and destabilization of the transition state. Additionally, the increased local polarity in the mutant allows for a larger number of water molecules to be present near the active site, effectively shielding the catalytic effect of the enzyme and contributing to the increased barrier.
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Affiliation(s)
- Gabriel Oanca
- Laboratory of Biocomputing and Bioinformatics, National Institute of Chemistry, Ljubljana, Slovenia.
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39
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Mavri J, Matute RA, Chu ZT, Vianello R. Path Integral Simulation of the H/D Kinetic Isotope Effect in Monoamine Oxidase B Catalyzed Decomposition of Dopamine. J Phys Chem B 2016; 120:3488-92. [DOI: 10.1021/acs.jpcb.6b00894] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Janez Mavri
- Laboratory
for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI−1000 Ljubljana, Slovenia
| | - Ricardo A. Matute
- University of Southern California, Department of Chemistry
SGM 418, 3620 McClintock
Avenue Los Angeles, California 90089-1062, United States
| | - Zhen T. Chu
- University of Southern California, Department of Chemistry
SGM 418, 3620 McClintock
Avenue Los Angeles, California 90089-1062, United States
| | - Robert Vianello
- Computational
Organic Chemistry and Biochemistry Group, Ruđer Bošković Institute, Bijenička 54, HR−10000 Zagreb, Croatia
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40
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Kamachi T, Yoshizawa K. Low-Mode Conformational Search Method with Semiempirical Quantum Mechanical Calculations: Application to Enantioselective Organocatalysis. J Chem Inf Model 2016; 56:347-53. [DOI: 10.1021/acs.jcim.5b00671] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Takashi Kamachi
- Institute
for Materials Chemistry
and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Kazunari Yoshizawa
- Institute
for Materials Chemistry
and Engineering, Kyushu University, Fukuoka 819-0395, Japan
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41
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He X, Lin M, Guo J, Qu Z, Xu F. Experimental and simulation studies of polyarginines across the membrane of giant unilamellar vesicles. RSC Adv 2016. [DOI: 10.1039/c6ra02420c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Cell-penetrating peptides have widespread applications in biomedicine because of their capability to translocate across cell membranes alone or with cargos.
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Affiliation(s)
- XiaoCong He
- Key Laboratory of Thermo-Fluid Science and Engineering of Ministry of Education
- School of Energy and Power Engineering
- Xi'an Jiaotong University
- Xi'an 710049
- P.R. China
| | - Min Lin
- Bioinspired Engineering and Biomechanics Center (BEBC)
- Xi'an Jiaotong University
- Xi'an 710049
- P.R. China
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education
| | - Jun Guo
- Key Laboratory of Thermo-Fluid Science and Engineering of Ministry of Education
- School of Energy and Power Engineering
- Xi'an Jiaotong University
- Xi'an 710049
- P.R. China
| | - ZhiGuo Qu
- Key Laboratory of Thermo-Fluid Science and Engineering of Ministry of Education
- School of Energy and Power Engineering
- Xi'an Jiaotong University
- Xi'an 710049
- P.R. China
| | - Feng Xu
- Bioinspired Engineering and Biomechanics Center (BEBC)
- Xi'an Jiaotong University
- Xi'an 710049
- P.R. China
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education
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42
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Dumont E, Monari A. Understanding DNA under oxidative stress and sensitization: the role of molecular modeling. Front Chem 2015; 3:43. [PMID: 26236706 PMCID: PMC4500984 DOI: 10.3389/fchem.2015.00043] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/29/2015] [Indexed: 12/12/2022] Open
Abstract
DNA is constantly exposed to damaging threats coming from oxidative stress, i.e., from the presence of free radicals and reactive oxygen species. Sensitization from exogenous and endogenous compounds that strongly enhance the frequency of light-induced lesions also plays an important role. The experimental determination of DNA lesions, though a difficult subject, is somehow well established and allows to elucidate even extremely rare DNA lesions. In parallel, molecular modeling has become fundamental to clearly understand the fine mechanisms related to DNA defects induction. Indeed, it offers an unprecedented possibility to get access to an atomistic or even electronic resolution. Ab initio molecular dynamics may also describe the time-evolution of the molecular system and its reactivity. Yet the modeling of DNA (photo-)reactions does necessitate elaborate multi-scale methodologies to tackle a damage induction reactivity that takes place in a complex environment. The double-stranded DNA environment is first characterized by a very high flexibility, but also a strongly inhomogeneous electrostatic embedding. Additionally, one aims at capturing more subtle effects, such as the sequence selectivity which is of critical important for DNA damage. The structure and dynamics of the DNA/sensitizers complexes, as well as the photo-induced electron- and energy-transfer phenomena taking place upon sensitization, should be carefully modeled. Finally the factors inducing different repair ratios for different lesions should also be rationalized. In this review we will critically analyze the different computational strategies used to model DNA lesions. A clear picture of the complex interplay between reactivity and structural factors will be sketched. The use of proper multi-scale modeling leads to the in-depth comprehension of DNA lesions mechanisms and also to the rational design of new chemo-therapeutic agents.
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Affiliation(s)
- Elise Dumont
- Laboratoire de Chimie, UMR 5182 Centre National de la Recherche Scientifique, École Normale Supérieure de Lyon Lyon, France
| | - Antonio Monari
- Université de Lorraine - Nancy, Theory-Modeling-Simulation, Structure et Réactivité des Systèmes Moléculaires Complexes (SRSMC) Vandoeuvre-les-Nancy, France ; Centre National de la Recherche Scientifique, Theory-Modeling-Simulation, Structure et Réactivité des Systèmes Moléculaires Complexes (SRSMC) Vandoeuvre-les-Nancy, France
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43
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Affiliation(s)
- Fangqiang Zhu
- Department
of Physics, Indiana University - Purdue University, Indianapolis, Indiana 46202, United States
| | - Bo Chen
- Department
of Physics, University of Central Florida, Orlando, Florida 32816, United States
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44
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Zapata-Torres G, Fierro A, Barriga-González G, Salgado JC, Celis-Barros C. Revealing Monoamine Oxidase B Catalytic Mechanisms by Means of the Quantum Chemical Cluster Approach. J Chem Inf Model 2015; 55:1349-60. [PMID: 26091526 DOI: 10.1021/acs.jcim.5b00140] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Two of the possible catalytic mechanisms for neurotransmitter oxidative deamination by monoamine oxidase B (MAO B), namely, polar nucleophilic and hydride transfer, were addressed in order to comprehend the nature of their rate-determining step. The Quantum Chemical Cluster Approach was used to obtain transition states of MAO B complexed with phenylethylamine (PEA), benzylamine (BA), and p-nitrobenzylamine (NBA). The choice of these amines relies on their importance to address MAO B catalytic mechanisms so as to help us to answer questions such as why BA is a better substrate than NBA or how para-substitution affects substrate's reactivity. Transition states were later validated by comparison with the experimental free energy barriers. From a theoretical point of view, and according to the our reported transition states, their calculated barriers and structural and orbital differences obtained by us among these compounds, we propose that good substrates such as BA and PEA might follow the hydride transfer pathway while poor substrates such as NBA prefer the polar nucleophilic mechanism, which might suggest that MAO B can act by both mechanisms. The low free energy barriers for BA and PEA reflect the preference that MAO B has for hydride transfer over the polar nucleophilic mechanism when catalyzing the oxidative deamination of neurotransmitters.
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Affiliation(s)
- Gerald Zapata-Torres
- †Molecular Graphics Suite, Department of Inorganic and Analytical Chemistry, Faculty of Chemical and Pharmaceutical Sciences, University of Chile, Santiago, Chile
| | - Angélica Fierro
- ‡Facultad de Química, Departamento de Química Orgánica, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - German Barriga-González
- §Universidad Andres Bello, Facultad de Ciencias Exactas, Departamento de Ciencias Quimicas, Avenida República 275, 8370146 Santiago, Chile
| | - J Cristian Salgado
- ∥Laboratory of Process Modeling and Distributed Computing, Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 850, Santiago, Chile
| | - Cristian Celis-Barros
- §Universidad Andres Bello, Facultad de Ciencias Exactas, Departamento de Ciencias Quimicas, Avenida República 275, 8370146 Santiago, Chile
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45
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Pavlin M, Repič M, Vianello R, Mavri J. The Chemistry of Neurodegeneration: Kinetic Data and Their Implications. Mol Neurobiol 2015; 53:3400-3415. [PMID: 26081152 DOI: 10.1007/s12035-015-9284-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 06/03/2015] [Indexed: 01/01/2023]
Abstract
We collected experimental kinetic rate constants for chemical processes responsible for the development and progress of neurodegeneration, focused on the enzymatic and non-enzymatic degradation of amine neurotransmitters and their reactive and neurotoxic metabolites. A gross scheme of neurodegeneration on the molecular level is based on two pathways. Firstly, reactive species oxidise heavy atom ions, which enhances the interaction with alpha-synuclein, thus promoting its folding to the beta form and giving rise to insoluble amyloid plaques. The latter prevents the function of vesicular transport leading to gradual neuronal death. In the second pathway, radical species, OH(·) in particular, react with the methylene groups of the apolar part of the lipid bilayer of either the cell or mitochondrial wall, resulting in membrane leakage followed by dyshomeostasis, loss of resting potential and neuron death. Unlike all other central neural system (CNS)-relevant biogenic amines, dopamine and noradrenaline are capable of a non-enzymatic auto-oxidative reaction, which produces hydrogen peroxide. This reaction is not limited to the mitochondrial membrane where scavenging enzymes, such as catalase, are located. On the other hand, dopamine and its metabolites, such as dopamine-o-quinone, dopaminechrome, 5,6-dihydroxyindole and indo-5,6-quinone, also interact directly with alpha-synuclein and reversibly inhibit plaque formation. We consider the role of the heavy metal ions, selected scavengers and scavenging enzymes, and discuss the relevance of certain foods and food supplements, including curcumin, garlic, N-acetyl cysteine, caffeine and red wine, as well as the long-term administration of non-steroid anti-inflammatory drugs and occasional tobacco smoking, that could all act toward preventing neurodegeneration. The current analysis can be employed in developing strategies for the prevention and treatment of neurodegeneration, and, hopefully, aid in the building of an overall kinetic molecular model of neurodegeneration itself.
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Affiliation(s)
- Matic Pavlin
- Computational Biophysics, German Research School for Simulation Sciences, Joint Venture of RWTH Aachen University and Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Computational Biomedicine, Institute for Advanced Simulations (IAS-5/INM-9), 52425, Jülich, Germany
| | - Matej Repič
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Robert Vianello
- Quantum Organic Chemistry Group, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia.
| | - Janez Mavri
- National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia.
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Zenn RK, Abad E, Kästner J. Influence of the Environment on the Oxidative Deamination of p-Substituted Benzylamines in Monoamine Oxidase. J Phys Chem B 2015; 119:3678-86. [DOI: 10.1021/jp512470a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Roland K. Zenn
- Institute of Theoretical
Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Enrique Abad
- Institute of Theoretical
Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Johannes Kästner
- Institute of Theoretical
Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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47
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Khodarahmi G, Asadi P, Farrokhpour H, Hassanzadeh F, Dinari M. Design of novel potential aromatase inhibitors via hybrid pharmacophore approach: docking improvement using the QM/MM method. RSC Adv 2015. [DOI: 10.1039/c5ra10097f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
QM/MM and docking methods were used for designing novel hybrid aromatase inhibitors incorporating benzofuran, imidazole and quinazolinone moieties.
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Affiliation(s)
- Ghadamali Khodarahmi
- Department of Medicinal Chemistry
- School of Pharmacy and Pharmaceutical Sciences
- Isfahan University of Medical Sciences
- Isfahan
- I. R. Iran
| | - Parvin Asadi
- Department of Medicinal Chemistry
- School of Pharmacy and Pharmaceutical Sciences
- Isfahan University of Medical Sciences
- Isfahan
- I. R. Iran
| | | | - Farshid Hassanzadeh
- Department of Medicinal Chemistry
- School of Pharmacy and Pharmaceutical Sciences
- Isfahan University of Medical Sciences
- Isfahan
- I. R. Iran
| | - Mohammad Dinari
- Department of Chemistry
- Isfahan University of Technology
- Isfahan
- I. R. Iran
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48
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Liu DM, Chen J, Shi YP. An online immobilized α-glucosidase microreactor for enzyme kinetics and inhibition assays. RSC Adv 2015. [DOI: 10.1039/c5ra07982a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
A novel online α-glucosidase-immobilized microreactor was developed by immobilizing α-glucosidase on capillary inner wall. The microreactor combination with capillary electrophoresis was applied in studying enzyme kinetics and inhibition kinetics.
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Affiliation(s)
- Dong-Mei Liu
- Key Laboratory of Chemistry of Northwestern Plant Resources
- Key Laboratory for Natural Medicine of Gansu Province
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou 730000
| | - Juan Chen
- Key Laboratory of Chemistry of Northwestern Plant Resources
- Key Laboratory for Natural Medicine of Gansu Province
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou 730000
| | - Yan-Ping Shi
- Key Laboratory of Chemistry of Northwestern Plant Resources
- Key Laboratory for Natural Medicine of Gansu Province
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou 730000
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